Starting phenix.real_space_refine on Thu May 15 05:30:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ems_28263/05_2025/8ems_28263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ems_28263/05_2025/8ems_28263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ems_28263/05_2025/8ems_28263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ems_28263/05_2025/8ems_28263.map" model { file = "/net/cci-nas-00/data/ceres_data/8ems_28263/05_2025/8ems_28263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ems_28263/05_2025/8ems_28263.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 56 5.16 5 C 8154 2.51 5 N 2152 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12688 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6329 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 29, 'TRANS': 750} Chain breaks: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Restraints were copied for chains: B Time building chain proxies: 13.12, per 1000 atoms: 1.03 Number of scatterers: 12688 At special positions: 0 Unit cell: (130.68, 102.6, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 2 15.00 O 2324 8.00 N 2152 7.00 C 8154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 59.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 47 through 72 removed outlier: 4.555A pdb=" N GLY B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.023A pdb=" N LEU B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.600A pdb=" N MET B 197 " --> pdb=" O PRO B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 268 through 274 removed outlier: 4.316A pdb=" N ALA B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 313 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.542A pdb=" N ALA B 343 " --> pdb=" O THR B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.729A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 396 Processing helix chain 'B' and resid 396 through 418 removed outlier: 3.645A pdb=" N LEU B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.591A pdb=" N ARG B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.678A pdb=" N LEU B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 496 through 508 removed outlier: 3.520A pdb=" N LYS B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 514 through 525 removed outlier: 3.591A pdb=" N SER B 523 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 554 removed outlier: 4.136A pdb=" N LEU B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 593 removed outlier: 4.025A pdb=" N ASN B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 632 removed outlier: 3.550A pdb=" N LYS B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 657 removed outlier: 3.639A pdb=" N LYS B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 660 No H-bonds generated for 'chain 'B' and resid 658 through 660' Processing helix chain 'B' and resid 676 through 684 Processing helix chain 'B' and resid 694 through 704 removed outlier: 4.465A pdb=" N GLU B 698 " --> pdb=" O GLY B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 708 Processing helix chain 'B' and resid 714 through 725 Processing helix chain 'B' and resid 727 through 734 removed outlier: 4.065A pdb=" N TYR B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 776 through 792 Processing helix chain 'B' and resid 793 through 807 Processing helix chain 'B' and resid 808 through 811 Processing helix chain 'B' and resid 812 through 824 removed outlier: 3.678A pdb=" N THR B 816 " --> pdb=" O SER B 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 47 through 72 removed outlier: 4.555A pdb=" N GLY A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.023A pdb=" N LEU A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.600A pdb=" N MET A 197 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 268 through 274 removed outlier: 4.316A pdb=" N ALA A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 313 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 340 through 343 removed outlier: 3.542A pdb=" N ALA A 343 " --> pdb=" O THR A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.730A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 Processing helix chain 'A' and resid 396 through 418 removed outlier: 3.644A pdb=" N LEU A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.591A pdb=" N ARG A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.678A pdb=" N LEU A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 496 through 508 removed outlier: 3.520A pdb=" N LYS A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.591A pdb=" N SER A 523 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 554 removed outlier: 4.136A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 removed outlier: 4.025A pdb=" N ASN A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 632 removed outlier: 3.550A pdb=" N LYS A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.640A pdb=" N LYS A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 660 No H-bonds generated for 'chain 'A' and resid 658 through 660' Processing helix chain 'A' and resid 676 through 684 Processing helix chain 'A' and resid 694 through 704 removed outlier: 4.466A pdb=" N GLU A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 708 Processing helix chain 'A' and resid 714 through 725 Processing helix chain 'A' and resid 727 through 734 removed outlier: 4.065A pdb=" N TYR A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 747 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 808 through 811 Processing helix chain 'A' and resid 812 through 824 removed outlier: 3.677A pdb=" N THR A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 202 removed outlier: 7.135A pdb=" N ALA B 154 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG B 242 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B 156 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TRP B 244 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY B 158 " --> pdb=" O TRP B 244 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ALA B 246 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ASN B 453 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 374 " --> pdb=" O ASN B 453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 171 Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AA4, first strand: chain 'B' and resid 386 through 388 Processing sheet with id=AA5, first strand: chain 'B' and resid 640 through 643 removed outlier: 3.771A pdb=" N LYS B 641 " --> pdb=" O ARG B 601 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N MET B 562 " --> pdb=" O THR B 602 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE B 604 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 564 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY B 606 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN B 566 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL B 567 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 202 removed outlier: 7.135A pdb=" N ALA A 154 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG A 242 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY A 156 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TRP A 244 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A 158 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ALA A 246 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N ASN A 453 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR A 374 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 171 Processing sheet with id=AA8, first strand: chain 'A' and resid 205 through 208 Processing sheet with id=AA9, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 643 removed outlier: 3.771A pdb=" N LYS A 641 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET A 562 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A 604 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP A 564 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY A 606 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN A 566 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL A 567 " --> pdb=" O GLU A 664 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4110 1.34 - 1.46: 2483 1.46 - 1.58: 6269 1.58 - 1.69: 2 1.69 - 1.81: 100 Bond restraints: 12964 Sorted by residual: bond pdb=" CA VAL B 59 " pdb=" C VAL B 59 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.30e-02 5.92e+03 8.18e-01 bond pdb=" CA VAL A 59 " pdb=" C VAL A 59 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.30e-02 5.92e+03 8.18e-01 bond pdb=" N GLN B 480 " pdb=" CA GLN B 480 " ideal model delta sigma weight residual 1.456 1.469 -0.013 1.44e-02 4.82e+03 8.05e-01 bond pdb=" CA LYS B 482 " pdb=" C LYS B 482 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.14e-02 7.69e+03 8.00e-01 bond pdb=" N GLN A 480 " pdb=" CA GLN A 480 " ideal model delta sigma weight residual 1.456 1.468 -0.012 1.44e-02 4.82e+03 7.05e-01 ... (remaining 12959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 16889 1.18 - 2.37: 492 2.37 - 3.55: 107 3.55 - 4.74: 27 4.74 - 5.92: 13 Bond angle restraints: 17528 Sorted by residual: angle pdb=" C ILE A 165 " pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C ILE B 165 " pdb=" N PHE B 166 " pdb=" CA PHE B 166 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" N ARG B 292 " pdb=" CA ARG B 292 " pdb=" CB ARG B 292 " ideal model delta sigma weight residual 114.17 110.71 3.46 1.14e+00 7.69e-01 9.22e+00 angle pdb=" N ARG A 292 " pdb=" CA ARG A 292 " pdb=" CB ARG A 292 " ideal model delta sigma weight residual 114.17 110.73 3.44 1.14e+00 7.69e-01 9.09e+00 angle pdb=" N GLN A 480 " pdb=" CA GLN A 480 " pdb=" C GLN A 480 " ideal model delta sigma weight residual 109.18 113.23 -4.05 1.42e+00 4.96e-01 8.12e+00 ... (remaining 17523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 7027 16.62 - 33.24: 617 33.24 - 49.86: 132 49.86 - 66.48: 12 66.48 - 83.10: 10 Dihedral angle restraints: 7798 sinusoidal: 3224 harmonic: 4574 Sorted by residual: dihedral pdb=" CA ILE B 165 " pdb=" C ILE B 165 " pdb=" N PHE B 166 " pdb=" CA PHE B 166 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ILE A 165 " pdb=" C ILE A 165 " pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG B 292 " pdb=" C ARG B 292 " pdb=" N LEU B 293 " pdb=" CA LEU B 293 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1771 0.072 - 0.144: 147 0.144 - 0.216: 2 0.216 - 0.288: 0 0.288 - 0.360: 2 Chirality restraints: 1922 Sorted by residual: chirality pdb=" CB ILE B 165 " pdb=" CA ILE B 165 " pdb=" CG1 ILE B 165 " pdb=" CG2 ILE B 165 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE A 165 " pdb=" CA ILE A 165 " pdb=" CG1 ILE A 165 " pdb=" CG2 ILE A 165 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA LYS B 482 " pdb=" N LYS B 482 " pdb=" C LYS B 482 " pdb=" CB LYS B 482 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 1919 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 292 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C ARG B 292 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG B 292 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 293 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 292 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C ARG A 292 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG A 292 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 293 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 90 " 0.013 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR A 90 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 90 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 90 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 90 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 90 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 90 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 90 " 0.001 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1560 2.75 - 3.29: 12239 3.29 - 3.83: 21711 3.83 - 4.36: 26772 4.36 - 4.90: 45066 Nonbonded interactions: 107348 Sorted by model distance: nonbonded pdb=" O PHE B 311 " pdb=" OG SER B 314 " model vdw 2.217 3.040 nonbonded pdb=" O PHE A 311 " pdb=" OG SER A 314 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN A 71 " pdb=" OG1 THR A 240 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLN B 71 " pdb=" OG1 THR B 240 " model vdw 2.225 3.040 nonbonded pdb=" OE1 GLU A 664 " pdb=" OH TYR A 780 " model vdw 2.278 3.040 ... (remaining 107343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.340 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.373 12966 Z= 0.479 Angle : 0.530 5.922 17528 Z= 0.294 Chirality : 0.042 0.360 1922 Planarity : 0.003 0.040 2240 Dihedral : 13.281 83.104 4842 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1544 helix: 0.99 (0.18), residues: 828 sheet: -0.70 (0.38), residues: 166 loop : -1.33 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 491 HIS 0.002 0.001 HIS A 614 PHE 0.015 0.001 PHE A 298 TYR 0.025 0.002 TYR A 90 ARG 0.003 0.000 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.16679 ( 663) hydrogen bonds : angle 6.31272 ( 1845) covalent geometry : bond 0.00262 (12964) covalent geometry : angle 0.53047 (17528) Misc. bond : bond 0.37233 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 1.394 Fit side-chains REVERT: B 764 MET cc_start: 0.7291 (tmm) cc_final: 0.7063 (tmt) REVERT: B 827 VAL cc_start: 0.7493 (t) cc_final: 0.7105 (m) REVERT: A 547 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6782 (mm-40) REVERT: A 827 VAL cc_start: 0.7492 (t) cc_final: 0.7111 (m) outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 1.2754 time to fit residues: 299.3760 Evaluate side-chains 176 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.193539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.176523 restraints weight = 12864.053| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.17 r_work: 0.3982 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12966 Z= 0.146 Angle : 0.560 5.576 17528 Z= 0.295 Chirality : 0.042 0.234 1922 Planarity : 0.004 0.039 2240 Dihedral : 4.960 41.499 1702 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.32 % Allowed : 9.68 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1544 helix: 1.06 (0.18), residues: 816 sheet: -0.37 (0.36), residues: 190 loop : -0.97 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 365 HIS 0.004 0.001 HIS A 399 PHE 0.017 0.002 PHE B 166 TYR 0.027 0.002 TYR A 297 ARG 0.003 0.000 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 663) hydrogen bonds : angle 5.04368 ( 1845) covalent geometry : bond 0.00330 (12964) covalent geometry : angle 0.55984 (17528) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.368 Fit side-chains REVERT: B 90 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6609 (t80) REVERT: B 126 GLU cc_start: 0.6189 (tt0) cc_final: 0.5924 (tt0) REVERT: B 764 MET cc_start: 0.7387 (tmm) cc_final: 0.7064 (tmt) REVERT: B 827 VAL cc_start: 0.7574 (t) cc_final: 0.7102 (m) REVERT: A 90 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6626 (t80) REVERT: A 126 GLU cc_start: 0.6178 (tt0) cc_final: 0.5762 (tt0) REVERT: A 827 VAL cc_start: 0.7580 (t) cc_final: 0.7109 (m) outliers start: 18 outliers final: 9 residues processed: 178 average time/residue: 1.2796 time to fit residues: 247.6724 Evaluate side-chains 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 599 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.191342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.174192 restraints weight = 12986.456| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.17 r_work: 0.3952 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12966 Z= 0.175 Angle : 0.594 5.891 17528 Z= 0.312 Chirality : 0.043 0.165 1922 Planarity : 0.004 0.035 2240 Dihedral : 5.135 43.458 1702 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.13 % Allowed : 12.32 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1544 helix: 0.88 (0.18), residues: 824 sheet: -0.37 (0.35), residues: 190 loop : -0.98 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 365 HIS 0.005 0.001 HIS B 399 PHE 0.017 0.002 PHE B 166 TYR 0.037 0.002 TYR A 297 ARG 0.004 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 663) hydrogen bonds : angle 5.03352 ( 1845) covalent geometry : bond 0.00401 (12964) covalent geometry : angle 0.59381 (17528) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.362 Fit side-chains REVERT: B 90 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6541 (t80) REVERT: B 385 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: B 706 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6433 (pp20) REVERT: B 764 MET cc_start: 0.7449 (tmm) cc_final: 0.7139 (tmt) REVERT: B 827 VAL cc_start: 0.7659 (t) cc_final: 0.7176 (m) REVERT: A 90 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6556 (t80) REVERT: A 385 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: A 689 ILE cc_start: 0.7703 (tt) cc_final: 0.7278 (pp) REVERT: A 706 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6366 (pp20) REVERT: A 827 VAL cc_start: 0.7663 (t) cc_final: 0.7176 (m) outliers start: 29 outliers final: 11 residues processed: 175 average time/residue: 1.2859 time to fit residues: 245.5290 Evaluate side-chains 171 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 706 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 137 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.176497 restraints weight = 12886.312| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.16 r_work: 0.3978 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12966 Z= 0.126 Angle : 0.523 5.409 17528 Z= 0.276 Chirality : 0.041 0.142 1922 Planarity : 0.003 0.032 2240 Dihedral : 4.943 43.199 1702 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.20 % Allowed : 13.93 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1544 helix: 1.16 (0.18), residues: 814 sheet: -0.18 (0.36), residues: 190 loop : -0.96 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 365 HIS 0.003 0.001 HIS B 34 PHE 0.014 0.001 PHE A 166 TYR 0.036 0.002 TYR B 297 ARG 0.004 0.000 ARG A 601 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 663) hydrogen bonds : angle 4.79450 ( 1845) covalent geometry : bond 0.00286 (12964) covalent geometry : angle 0.52343 (17528) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.464 Fit side-chains REVERT: B 84 TYR cc_start: 0.7325 (t80) cc_final: 0.7035 (t80) REVERT: B 90 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6485 (t80) REVERT: B 385 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 506 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6320 (mptt) REVERT: B 706 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6428 (pp20) REVERT: B 764 MET cc_start: 0.7423 (tmm) cc_final: 0.7082 (tmt) REVERT: B 789 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6868 (mp-120) REVERT: B 827 VAL cc_start: 0.7581 (t) cc_final: 0.7106 (m) REVERT: A 84 TYR cc_start: 0.7329 (t80) cc_final: 0.7006 (t80) REVERT: A 90 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6495 (t80) REVERT: A 385 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: A 506 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6441 (mptt) REVERT: A 706 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6436 (pp20) REVERT: A 827 VAL cc_start: 0.7590 (t) cc_final: 0.7107 (m) outliers start: 30 outliers final: 13 residues processed: 169 average time/residue: 1.3058 time to fit residues: 239.8706 Evaluate side-chains 170 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 722 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.175034 restraints weight = 12938.850| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.18 r_work: 0.3963 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12966 Z= 0.150 Angle : 0.564 5.642 17528 Z= 0.296 Chirality : 0.042 0.153 1922 Planarity : 0.004 0.033 2240 Dihedral : 5.048 45.091 1702 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.49 % Allowed : 14.37 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1544 helix: 1.05 (0.18), residues: 820 sheet: -0.23 (0.36), residues: 190 loop : -0.97 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 365 HIS 0.004 0.001 HIS A 34 PHE 0.016 0.002 PHE A 166 TYR 0.039 0.002 TYR A 297 ARG 0.005 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 663) hydrogen bonds : angle 4.83575 ( 1845) covalent geometry : bond 0.00345 (12964) covalent geometry : angle 0.56400 (17528) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.558 Fit side-chains REVERT: B 90 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6488 (t80) REVERT: B 205 LYS cc_start: 0.6777 (mmmt) cc_final: 0.6073 (mptt) REVERT: B 385 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: B 601 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5706 (mtm180) REVERT: B 706 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6433 (pp20) REVERT: B 764 MET cc_start: 0.7474 (tmm) cc_final: 0.7233 (tmt) REVERT: B 789 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6908 (mp-120) REVERT: B 827 VAL cc_start: 0.7671 (t) cc_final: 0.7184 (m) REVERT: A 90 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6501 (t80) REVERT: A 234 MET cc_start: 0.6884 (mmm) cc_final: 0.6628 (mmm) REVERT: A 385 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: A 689 ILE cc_start: 0.7923 (tt) cc_final: 0.7474 (pp) REVERT: A 706 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: A 789 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6840 (mp-120) REVERT: A 827 VAL cc_start: 0.7680 (t) cc_final: 0.7182 (m) outliers start: 34 outliers final: 13 residues processed: 175 average time/residue: 1.2207 time to fit residues: 233.1236 Evaluate side-chains 171 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.176360 restraints weight = 12959.756| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.18 r_work: 0.3978 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12966 Z= 0.130 Angle : 0.536 6.935 17528 Z= 0.282 Chirality : 0.041 0.153 1922 Planarity : 0.003 0.032 2240 Dihedral : 4.964 45.196 1702 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.13 % Allowed : 14.66 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1544 helix: 1.13 (0.18), residues: 824 sheet: -0.09 (0.37), residues: 190 loop : -0.93 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 365 HIS 0.004 0.001 HIS B 34 PHE 0.015 0.001 PHE A 166 TYR 0.034 0.002 TYR A 297 ARG 0.004 0.000 ARG A 601 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 663) hydrogen bonds : angle 4.74416 ( 1845) covalent geometry : bond 0.00298 (12964) covalent geometry : angle 0.53622 (17528) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.500 Fit side-chains REVERT: B 171 ARG cc_start: 0.6892 (mpt-90) cc_final: 0.6674 (mpt-90) REVERT: B 197 MET cc_start: 0.6500 (ttt) cc_final: 0.6138 (tmm) REVERT: B 385 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: B 706 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: B 764 MET cc_start: 0.7451 (tmm) cc_final: 0.7219 (tmt) REVERT: B 789 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6873 (mp-120) REVERT: B 827 VAL cc_start: 0.7686 (t) cc_final: 0.7175 (m) REVERT: A 29 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6795 (mtmp) REVERT: A 171 ARG cc_start: 0.6886 (mpt-90) cc_final: 0.6666 (mpt-90) REVERT: A 205 LYS cc_start: 0.6421 (mmmt) cc_final: 0.6087 (mmmm) REVERT: A 385 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: A 706 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6419 (pp20) REVERT: A 789 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6821 (mp-120) REVERT: A 827 VAL cc_start: 0.7693 (t) cc_final: 0.7180 (m) outliers start: 29 outliers final: 14 residues processed: 165 average time/residue: 1.3217 time to fit residues: 236.9797 Evaluate side-chains 168 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.193972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176856 restraints weight = 12771.692| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.17 r_work: 0.3987 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12966 Z= 0.123 Angle : 0.521 6.026 17528 Z= 0.276 Chirality : 0.041 0.152 1922 Planarity : 0.003 0.031 2240 Dihedral : 4.917 45.363 1702 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.27 % Allowed : 15.25 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1544 helix: 1.18 (0.18), residues: 824 sheet: -0.07 (0.37), residues: 190 loop : -0.92 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 365 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.001 PHE A 166 TYR 0.037 0.002 TYR A 297 ARG 0.004 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 663) hydrogen bonds : angle 4.72724 ( 1845) covalent geometry : bond 0.00284 (12964) covalent geometry : angle 0.52136 (17528) Misc. bond : bond 0.00054 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.309 Fit side-chains REVERT: B 165 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.4873 (tp) REVERT: B 197 MET cc_start: 0.6425 (ttt) cc_final: 0.6158 (tmm) REVERT: B 205 LYS cc_start: 0.6570 (mmmt) cc_final: 0.6215 (mmmm) REVERT: B 385 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: B 601 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5660 (mtm180) REVERT: B 706 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6409 (pp20) REVERT: B 764 MET cc_start: 0.7463 (tmm) cc_final: 0.7106 (tmt) REVERT: B 789 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6833 (mp-120) REVERT: B 827 VAL cc_start: 0.7681 (t) cc_final: 0.7172 (m) REVERT: A 29 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6790 (mtmp) REVERT: A 84 TYR cc_start: 0.7261 (t80) cc_final: 0.6983 (t80) REVERT: A 165 ILE cc_start: 0.5571 (OUTLIER) cc_final: 0.4869 (tp) REVERT: A 205 LYS cc_start: 0.6430 (mmmt) cc_final: 0.6101 (mmmm) REVERT: A 385 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: A 689 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7463 (pp) REVERT: A 706 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6390 (pp20) REVERT: A 789 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6842 (mp-120) REVERT: A 827 VAL cc_start: 0.7689 (t) cc_final: 0.7183 (m) outliers start: 31 outliers final: 13 residues processed: 164 average time/residue: 1.2964 time to fit residues: 231.9246 Evaluate side-chains 171 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 133 optimal weight: 3.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.197700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180727 restraints weight = 12834.839| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.18 r_work: 0.4024 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12966 Z= 0.102 Angle : 0.489 6.605 17528 Z= 0.260 Chirality : 0.039 0.139 1922 Planarity : 0.003 0.029 2240 Dihedral : 4.700 43.746 1702 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.69 % Allowed : 16.06 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1544 helix: 1.39 (0.18), residues: 826 sheet: 0.08 (0.37), residues: 190 loop : -0.79 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 365 HIS 0.002 0.001 HIS A 34 PHE 0.014 0.001 PHE B 298 TYR 0.030 0.001 TYR B 297 ARG 0.003 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 663) hydrogen bonds : angle 4.57440 ( 1845) covalent geometry : bond 0.00235 (12964) covalent geometry : angle 0.48878 (17528) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.480 Fit side-chains REVERT: B 84 TYR cc_start: 0.7197 (t80) cc_final: 0.6971 (t80) REVERT: B 197 MET cc_start: 0.6419 (ttt) cc_final: 0.6182 (tmm) REVERT: B 385 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: B 601 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5657 (mtm180) REVERT: B 706 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6597 (pp20) REVERT: B 759 LYS cc_start: 0.7627 (mptt) cc_final: 0.6750 (pmtt) REVERT: B 764 MET cc_start: 0.7411 (tmm) cc_final: 0.7074 (tmt) REVERT: B 827 VAL cc_start: 0.7681 (t) cc_final: 0.7147 (m) REVERT: A 205 LYS cc_start: 0.6328 (mmmt) cc_final: 0.6020 (mmmm) REVERT: A 385 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: A 689 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7452 (pp) REVERT: A 706 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6572 (pp20) REVERT: A 759 LYS cc_start: 0.7630 (mptt) cc_final: 0.7170 (ttpp) REVERT: A 827 VAL cc_start: 0.7679 (t) cc_final: 0.7139 (m) outliers start: 23 outliers final: 10 residues processed: 171 average time/residue: 1.3172 time to fit residues: 244.9675 Evaluate side-chains 162 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 706 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 152 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.177959 restraints weight = 12806.012| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.18 r_work: 0.3988 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12966 Z= 0.128 Angle : 0.537 8.819 17528 Z= 0.283 Chirality : 0.041 0.156 1922 Planarity : 0.003 0.030 2240 Dihedral : 4.855 46.220 1702 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.76 % Allowed : 16.35 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1544 helix: 1.32 (0.18), residues: 822 sheet: -0.02 (0.37), residues: 190 loop : -0.78 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 365 HIS 0.003 0.001 HIS A 582 PHE 0.016 0.001 PHE B 166 TYR 0.036 0.002 TYR B 297 ARG 0.004 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 663) hydrogen bonds : angle 4.66750 ( 1845) covalent geometry : bond 0.00296 (12964) covalent geometry : angle 0.53671 (17528) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.435 Fit side-chains REVERT: B 165 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.4861 (tp) REVERT: B 171 ARG cc_start: 0.6693 (mpt-90) cc_final: 0.6492 (mpt-90) REVERT: B 205 LYS cc_start: 0.6552 (mmmt) cc_final: 0.6213 (mmmm) REVERT: B 385 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: B 601 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5690 (mtm180) REVERT: B 706 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6401 (pp20) REVERT: B 759 LYS cc_start: 0.7675 (mptt) cc_final: 0.6772 (pmtt) REVERT: B 764 MET cc_start: 0.7458 (tmm) cc_final: 0.7101 (tmt) REVERT: B 827 VAL cc_start: 0.7645 (t) cc_final: 0.7140 (m) REVERT: A 29 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6778 (mtmp) REVERT: A 165 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.4861 (tp) REVERT: A 171 ARG cc_start: 0.6698 (mpt-90) cc_final: 0.6493 (mpt-90) REVERT: A 205 LYS cc_start: 0.6419 (mmmt) cc_final: 0.5835 (mptt) REVERT: A 385 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: A 689 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7421 (pp) REVERT: A 706 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6568 (pp20) REVERT: A 759 LYS cc_start: 0.7688 (mptt) cc_final: 0.6783 (pmtt) REVERT: A 789 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6856 (mp-120) REVERT: A 827 VAL cc_start: 0.7656 (t) cc_final: 0.7141 (m) outliers start: 24 outliers final: 10 residues processed: 166 average time/residue: 1.3140 time to fit residues: 236.9737 Evaluate side-chains 173 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.194809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.177606 restraints weight = 12842.618| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.18 r_work: 0.3986 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12966 Z= 0.131 Angle : 0.550 9.125 17528 Z= 0.290 Chirality : 0.041 0.159 1922 Planarity : 0.003 0.030 2240 Dihedral : 4.928 47.082 1702 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.76 % Allowed : 16.50 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1544 helix: 1.28 (0.18), residues: 822 sheet: -0.05 (0.36), residues: 190 loop : -0.81 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 365 HIS 0.003 0.001 HIS B 34 PHE 0.016 0.001 PHE B 166 TYR 0.047 0.002 TYR A 297 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 663) hydrogen bonds : angle 4.70470 ( 1845) covalent geometry : bond 0.00304 (12964) covalent geometry : angle 0.54958 (17528) Misc. bond : bond 0.00055 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.449 Fit side-chains REVERT: B 165 ILE cc_start: 0.5588 (OUTLIER) cc_final: 0.4870 (tp) REVERT: B 171 ARG cc_start: 0.6722 (mpt-90) cc_final: 0.6514 (mpt-90) REVERT: B 205 LYS cc_start: 0.6567 (mmmt) cc_final: 0.6228 (mmmm) REVERT: B 385 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: B 601 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5677 (mtm180) REVERT: B 706 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6440 (pp20) REVERT: B 759 LYS cc_start: 0.7704 (mptt) cc_final: 0.6798 (pmtt) REVERT: B 764 MET cc_start: 0.7478 (tmm) cc_final: 0.7157 (tmt) REVERT: B 827 VAL cc_start: 0.7671 (t) cc_final: 0.7157 (m) REVERT: A 29 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6791 (mtmp) REVERT: A 165 ILE cc_start: 0.5580 (OUTLIER) cc_final: 0.4859 (tp) REVERT: A 171 ARG cc_start: 0.6735 (mpt-90) cc_final: 0.6520 (mpt-90) REVERT: A 385 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: A 689 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7395 (pp) REVERT: A 706 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6414 (pp20) REVERT: A 759 LYS cc_start: 0.7707 (mptt) cc_final: 0.6790 (pmtt) REVERT: A 789 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6818 (mp-120) REVERT: A 827 VAL cc_start: 0.7678 (t) cc_final: 0.7169 (m) outliers start: 24 outliers final: 11 residues processed: 164 average time/residue: 1.2807 time to fit residues: 228.2211 Evaluate side-chains 171 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 50 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.197175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.180355 restraints weight = 12843.110| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.16 r_work: 0.4023 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12966 Z= 0.108 Angle : 0.518 9.171 17528 Z= 0.274 Chirality : 0.040 0.161 1922 Planarity : 0.003 0.029 2240 Dihedral : 4.782 46.021 1702 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.69 % Allowed : 16.57 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1544 helix: 1.44 (0.18), residues: 822 sheet: 0.01 (0.36), residues: 190 loop : -0.74 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 365 HIS 0.002 0.001 HIS B 34 PHE 0.014 0.001 PHE A 298 TYR 0.038 0.001 TYR A 297 ARG 0.003 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 663) hydrogen bonds : angle 4.59067 ( 1845) covalent geometry : bond 0.00250 (12964) covalent geometry : angle 0.51770 (17528) Misc. bond : bond 0.00035 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8218.65 seconds wall clock time: 142 minutes 21.71 seconds (8541.71 seconds total)